Variant report

Variant	rs60653099
Chromosome Location	chr2:99801086-99801087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr2:99800975-99801174	HepG2	liver:	n/a	n/a
2	MAFK	chr2:99801010-99801109	HepG2	liver:	n/a	chr2:99801055-99801070
3	MAFK	chr2:99800984-99801143	HepG2	liver:	n/a	chr2:99801055-99801070

No.	Distal block	Cell Line	Cell type
1	chr2:99796817..99802176-chr2:99802213..99807656,6	MCF-7	breast:
2	chr2:99797861..99801159-chr2:99814018..99816783,5	MCF-7	breast:
3	chr2:99800478..99805908-chr2:99949969..99953911,6	MCF-7	breast:

Variant related genes	Relation type
MRPL30	TF binding region
MITD1	TF binding region
ENSG00000158417	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000185414	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10496334	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10496335	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123760	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123768	0.93[EUR][1000 genomes]
rs11526114	0.86[EUR][1000 genomes]
rs12233087	0.86[EUR][1000 genomes]
rs12620997	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1586434	0.86[EUR][1000 genomes]
rs17022180	0.83[ASN][1000 genomes]
rs17022249	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28785294	1.00[EUR][1000 genomes]
rs28794804	0.83[ASN][1000 genomes]
rs35071324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762472	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3791211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4850895	0.82[ASN][1000 genomes]
rs56926889	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57273701	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57743480	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58595226	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58635701	0.93[EUR][1000 genomes]
rs58745514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59252741	0.82[ASN][1000 genomes]
rs59506582	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60056452	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60516303	0.83[ASN][1000 genomes]
rs6719145	0.86[EUR][1000 genomes]
rs6746969	0.86[EUR][1000 genomes]
rs6748497	0.86[EUR][1000 genomes]
rs6749198	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7568749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9752510	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798400-99803600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:99798400-99803600	Weak transcription	Left Ventricle	heart
3	chr2:99798400-99807200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:99798400-99812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:99798600-99801600	Enhancers	Pancreas	Pancrea
6	chr2:99798600-99803000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:99798600-99803400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:99798600-99803400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr2:99798600-99803400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:99798600-99804600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:99798600-99805400	Weak transcription	Psoas Muscle	Psoas
12	chr2:99798600-99805600	Weak transcription	Brain Anterior Caudate	brain
13	chr2:99798600-99808000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:99798600-99808200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:99798600-99812000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:99798600-99812000	Weak transcription	Aorta	Aorta
17	chr2:99798600-99814000	Weak transcription	Right Ventricle	heart
18	chr2:99798600-99814800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:99798600-99815200	Weak transcription	Esophagus	oesophagus
20	chr2:99798600-99822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
22	chr2:99798800-99801400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:99798800-99801600	Enhancers	Dnd41	blood
24	chr2:99798800-99802600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:99798800-99802600	Weak transcription	Fetal Stomach	stomach
26	chr2:99798800-99802800	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:99798800-99803000	Weak transcription	HSMMtube	muscle
28	chr2:99798800-99803400	Weak transcription	Primary B cells from cord blood	blood
29	chr2:99798800-99803400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:99798800-99803400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:99798800-99803400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:99798800-99803400	Weak transcription	Spleen	Spleen
33	chr2:99798800-99803600	Weak transcription	Fetal Intestine Small	intestine
34	chr2:99798800-99804400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:99798800-99804800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:99798800-99805200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:99798800-99805400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:99798800-99805600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:99798800-99805600	Weak transcription	Brain Substantia Nigra	brain
40	chr2:99798800-99805600	Weak transcription	Colonic Mucosa	Colon
41	chr2:99798800-99805600	Weak transcription	Fetal Intestine Large	intestine
42	chr2:99798800-99805600	Weak transcription	NH-A	brain
43	chr2:99798800-99806400	Weak transcription	Thymus	Thymus
44	chr2:99798800-99806600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:99798800-99807800	Weak transcription	NHDF-Ad	bronchial
46	chr2:99798800-99810800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:99798800-99812000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:99798800-99812000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:99798800-99812000	Weak transcription	Fetal Kidney	kidney
50	chr2:99798800-99815400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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